Thermodynamic and Structural Analysis of DNA Damage Architectures Related to Replication

Table 2

Comparison of 𝑇_𝑚 values for replication relevant DNA architectures containing individual 3′ and 5′ overhangs, a terminal phosphate, and presence of both an overhang and phosphate. The presence of a 3′ or 5′ phosphate (PO₄), hydroxyl (OH) and a 6 mer overhang is indicated as an “X” or “Y” at the end of the core dsDNA sequences. Δ𝑇_𝑚 values were obtained by subtracting the 𝑇_𝑚 of each construct from the 𝑇_𝑚 value of the core duplex.

ID	Base Sequence		𝑇𝑚 (°C)	Δ𝑇𝑚 (°C)
1	5^′-CGCAACCTGAAAX
	3^′-GCGTTGGACTTTY
1G	X = OH	Y = OH	51.7 ± 0.2	—
1H	X = OH	Y = PO4	51.3 ± 0.0	−0.4^a
1I	X = AAAAAA	Y = OH	48.9 ± 0.3	−2.8^b
1J	X = AAAAAA	Y = PO4	47.9 ± 0.1	−3.4^b
				−1.0^a
1K	X = GACTGT	Y = OH	49.8 ± 0.3	−1.9^b
1L	X = GACTGT	Y = PO4	48.7 ± 0.2	−2.6^b
				−1.1^a
2	5^′-GCGTTGGACTTTX
	3^′-CGCAACCTGAAAY
2G	X = OH	Y = OH	52.9 ± 0.2	—
2H	X = PO4	Y = OH	52.0 ± 0.2	−0.9^a
2I	X = OH	Y = AAAAAA	51.8 ± 0.1	−1.1^b
2J	X = PO4	Y = AAAAAA	50.5 ± 0.3	−1.5^b
				−1.3^a
2K	X = OH	Y = GACTGT	51.6 ± 0.2	−1.3^b
2L	X = PO4	Y = GACTGT	50.4 ± 0.2	−1.6^b
				−1.2^a

aIndicates the Δ𝑇_𝑚 introduced by an individual phosphate. Δ𝑇_𝑚 was determined by subtracting substrate G from H, I from J and K from L. ^bIndicates the Δ𝑇_𝑚 introduced by an individual overhang. Δ𝑇_𝑚 was determined by subtracting substrate G from I, G from K, H from J, and H from L.